NEXUS File Format

In order for the parser to correctly extract all relevant information from your phylogeneitc tree, your NEXUS file must be in the exact format described below (most NEXUS files will already be in this format, but if you are having issues with your file being read properly, here is how to format it):


Two example NEXUS files are provided in the test/data folder : S10593.nex and E1E2L1.nex

An example sequence file is provided in the test/data folder : Example_Sequence.txt


generate_caos_rules("test/data/S10593.nex", "test/data")

This will generate your CAOS rules for the tree in the S10593.nex NEXUS file and place all output files from rule generation in the test/data directory.

tree, character_labels, taxa_labels = load_tree("test/data")

This will load the internal representation of the tree and CAOS rules from the files output during rule generation in the test/data directory.

classification = classify_new_sequence(tree, character_labels, taxa_labels, "test/data/Example_Sequence.txt", "test/data")

This will return the classification result, either a string with the classification label or a Node object (under classifiction).